A method of designing probes for detecting a target sequence and a method of detecting target sequence using the probes are provided. The method of designing probes for detecting target sequence includes: selecting an anchoring location in the target sequence, wherein the anchoring location is a location in the target sequence at which a first non-target sequence in a plurality of non-target sequences is different from the target sequence, wherein the first non-target sequence has a sequence similarity to the target sequence that is identical to or higher than the sequence similarity of other non-target sequences in the plurality of non-target sequences; selecting a first probe designing region, wherein the first probe designing region is a fixed region in the target sequence comprising the anchoring location; selecting a probe selection location, wherein the probe selection location is a location in the target sequence at which a second non-target sequence in the plurality of non-target sequences is different from the target sequence; selecting a matched probe, wherein the matched probe comprises a sequence complementary to the target sequence, wherein the probe selecting location is at the center of the sequence of the matched probe; and selecting a mismatched probe, wherein the mismatched probe is longer than the matched probe, wherein the mismatched probe comprises a sequence complementary to the target sequence at all locations except at a mismatched location, wherein the probe selection location is at a first location in the sequence of the mismatched probe and the mismatched location is at a second location in the sequence of the mismatched probe.
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